There's a lot of undue mystical properties given to these headphones, and most of the power requirements are just total nonsense, and hurts people new to these cans, or new to the hobby. I've owned the HE6se v2 three separate times, and the power requirements are overblown, and people who say it needs even more power to sound right, or needs more power to somehow mellow out are mistaken I think there's 2 possible factors to what you're experiencing.
First- Something about the actual frequency response irritates your ears, or brain. I'm a huge fan of EQ, and I would highly recommend using EQ with these, or any headphones, regardless of if you get headaches, or ear pain. There's a lot to be gained with EQ, and it's pretty much free no matter what platform you listen on.
I currently use several different EQ profiles, and sometimes modify them to my liking. But all of them sound better than the stock tuning. Most used are probably the ones from diyaudioheaven.com (a site ran by our awesome resident solderdude), oratory 1990, or Junki or Antroid from headphones.com. Again lots of eq profiles for this set, and all are better than stock, and you can tweak from there to try and eliminate your personal sensitivities
Second - Something about the fit of this headphone is absolutely the most uncomfortable headphone I've ever owned. I have the same headband on several other Hifiman headphones (edition xs) but I believe this crappy headband, combined with the high weight of the HE6SE v2 magnet structure makes them the worst of the bunch, and at times extremely painful. Sometimes I would get the direct center top hotspot, other times I would just get an overall headache from them. This manifested as just an overall aching sensation, not from a specific area, but most likely related to clamp force/ weight/ headband combination.
To solve this I'd recommend at a minimum, the 3d printed capra strap.
https://capraaudio.com/products/hifiman-comfort-strap This makes this headband way more tolerable, and I have no pain on my edition XS that I switched to this headband. The huge surface area helps a lot with heavy dual magnet planars like the HE-6. Easy to purchase from Capra, or have 3d printed locally. The 3d print files are free on their site if needed.
If you're willing to spend more (I would make sure you truly plan to keep these headphones) then I would recommend the hifiman comfort strap.
https://store.hifiman.com/index.php/the-newly-enhanced-comfort-headband.html The price is steep for the quality at $75.00 for fake leather and plastic, but it is WAY more comfortable, and looks nice as it's original hifiman.
You have to use a screw driver and disassemble them to install the official hifman strap, so please keep that in mind. TO me was well worth it, and totally eliminated any comfort issues I had with the HE6SE v2, no more headaches, no more hotspot, and I wear them for long multi-hour gaming sessions quite regularly.
Hope this helps as I personally really enjoy these headphones. I also do really enjoy my edition XS which are considerably cheaper, egg shape vs round which works better for some peoples heads, but also the Edition XS are significantly lighter, and easier to drive which suits a lot more people. I do think the HE-6 SE V2 are overall better, but just some food for thought.